fix(watch): schedule a sync when a directory is deleted (#1313)

A directory deletion arrives as ONE event on the directory's own path.
That path has no source extension, so handleChange dropped it at the
isSourceFile gate before ever scheduling a sync — and the files inside
may never get events of their own (Windows's recursive watcher reports
only the top-most removed entry; FSEvents can coalesce a tree deletion
the same way). Every child record then sat stale in the index until an
unrelated edit happened to trigger a sync (#1285).

A non-source path that no longer EXISTS on disk now schedules the
debounced sync; the sync's scan-diff removes whatever vanished (already
correct — verified: manual `codegraph sync` cascades fine). Events for
live non-source files stay fully ignored, so build churn schedules
nothing.

Fixes #1285

Co-authored-by: Claude Fable 5 <noreply@anthropic.com>

CHANGELOG.md

@@ -18,6 +18,7 @@ and adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ### Fixes
 
+- Deleting a whole directory is now picked up by watch mode: the files inside it are removed from the index on the next auto-sync instead of lingering as stale records until an unrelated edit happened to trigger one. Operating systems often report a directory deletion as a single event on the directory itself (with no per-file events for its contents), which the watcher previously discarded. (#1285)
 - `codegraph sync` now gets the same slow-disk fix that made full indexing fast in 1.4.0: database checkpointing is deferred for the whole incremental run instead of firing every few megabytes of writes. On mechanical drives and other high-latency storage, a small sync on a large index no longer stalls for minutes at near-zero CPU — the cost of a sync scales with what changed, not with the size of the existing index. The same `CODEGRAPH_NO_WAL_DEFER=1` switch turns it off. (#1248)
 - C functions declared with a project-specific attribute macro in front of a typedef'd return type (`SEC_ATTR UINT32 MyFunc(VOID)` — common in embedded and kernel code) are now indexed under their real names. Previously the parser tripped over the unknown macro and stored the parameter list as the function name, leaving entries like `"(VOID)"` in the graph and making the real function unfindable. (#1211)
 - C++ methods defined out-of-line inside a namespace (`namespace sim { Output MyClass::Apply(...) { ... } }`) now carry the namespace in their qualified name, matching their class. Fully-qualified call sites from other files (`sim::MyClass::Apply(...)`) resolve to the definition again, so `codegraph callers` and file impact no longer come up empty for this pattern. (#1291)